Variant report

Variant	rs2812308
Chromosome Location	chr9:108228745-108228746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108188025..108188833-chr9:108228643..108229576,2	MCF-7	breast:
2	chr9:108228659..108231354-chr9:108233201..108235205,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10115299	0.84[EUR][1000 genomes]
rs10761100	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10816278	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10820809	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10820810	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10820812	0.84[ASN][1000 genomes]
rs10820813	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1327354	0.92[ASN][1000 genomes]
rs1360089	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1806898	0.98[ASN][1000 genomes]
rs1815383	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1960023	0.85[ASN][1000 genomes]
rs1987634	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2225246	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2427769	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2518106	0.87[EUR][1000 genomes]
rs2518112	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2518114	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2518116	0.91[ASN][1000 genomes]
rs2518120	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2518123	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2518124	0.85[ASN][1000 genomes]
rs2518128	0.90[EUR][1000 genomes]
rs2518131	0.92[EUR][1000 genomes]
rs2768279	0.92[ASN][1000 genomes]
rs2768280	0.90[EUR][1000 genomes]
rs2768283	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2768290	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2768291	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2768292	0.85[ASN][1000 genomes]
rs2768294	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2771038	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2771041	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2771042	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2812297	0.82[ASN][1000 genomes]
rs2812303	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2812307	1.00[ASN][1000 genomes]
rs2812310	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4742650	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4742947	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4742948	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6477447	0.83[EUR][1000 genomes]
rs6477449	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7020083	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7357632	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
5	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108211000-108248000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:108212200-108234800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
4	chr9:108220200-108243400	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:108220400-108237400	Weak transcription	Brain Hippocampus Middle	brain
6	chr9:108220400-108252600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:108220600-108231000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:108220600-108237000	Weak transcription	Pancreas	Pancrea
9	chr9:108220600-108237400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:108220800-108229200	Weak transcription	NHLF	lung
11	chr9:108220800-108237000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:108220800-108237600	Weak transcription	Aorta	Aorta
13	chr9:108221000-108229000	Weak transcription	Lung	lung
14	chr9:108221000-108233200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr9:108221000-108235400	Weak transcription	Gastric	stomach
16	chr9:108221000-108236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:108221000-108237400	Weak transcription	Brain Substantia Nigra	brain
18	chr9:108221000-108257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:108221000-108257200	Weak transcription	Fetal Stomach	stomach
20	chr9:108221000-108266000	Weak transcription	NHEK	skin
21	chr9:108221000-108277200	Weak transcription	Left Ventricle	heart
22	chr9:108221200-108232800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:108221200-108235000	Weak transcription	Spleen	Spleen
24	chr9:108221400-108232200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr9:108221800-108236600	Weak transcription	Small Intestine	intestine
26	chr9:108221800-108238200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr9:108222000-108237600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr9:108222200-108237400	Weak transcription	Psoas Muscle	Psoas
29	chr9:108222200-108259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:108222200-108277000	Weak transcription	Ovary	ovary
31	chr9:108222400-108229800	Weak transcription	Fetal Intestine Small	intestine
32	chr9:108222400-108236800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr9:108222400-108242200	Weak transcription	Brain Anterior Caudate	brain
34	chr9:108222400-108259000	Weak transcription	HSMMtube	muscle
35	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
36	chr9:108223200-108252600	Weak transcription	K562	blood
37	chr9:108223600-108255200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr9:108224800-108244000	Weak transcription	Fetal Brain Male	brain
39	chr9:108225000-108237000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr9:108225000-108249200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr9:108225800-108233600	Strong transcription	A549	lung
42	chr9:108226400-108232200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:108226400-108232400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr9:108226400-108234800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:108226600-108229000	Strong transcription	Brain Germinal Matrix	brain
46	chr9:108226600-108233600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:108226600-108234000	Strong transcription	NHDF-Ad	bronchial
48	chr9:108226600-108235600	Strong transcription	HepG2	liver
49	chr9:108226800-108231800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr9:108226800-108235400	Strong transcription	HSMM	muscle

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